The oil palm (E. guineensis and E. oleifera) can be classified into separate groups based on its fruit characteristics, and has three naturally occurring fruit types which vary in shell thickness and oil yield. Dura type palms are homozygous for a wild type allele of the shell gene (sh+/sh+), have a thick seed coat or shell (2-8 mm) and produce approximately 5.3 tons of oil per hectare per year. Tenera type palms are heterozygous for a wild type and mutant allele of the shell gene (sh+/sh−), have a relatively thin shell surrounded by a distinct fiber ring, and produce approximately 7.4 tons of oil per hectare per year. Finally, pisifera type palms are homozygous for a mutant allele of the shell gene (sh−/sh−), have no seed coat or shell, and are usually female sterile (Hartley, 1988) (Table 1). Therefore, the inheritance of the single gene controlling shell phenotype is a major contributor to palm oil yield.
Tenera palms are hybrids between the dura and pisifera palms. Whitmore (1973) described the various fruit forms as different varieties of oil palm. However, Latiff (2000) was in agreement with Purseglove (1972) that varieties or cultivars as proposed by Whitmore (1973), do not occur in the strict sense in this species. As such, Latiff (2000) proposed the term “race” to differentiate dura, pisifera and tenera. Race was considered an appropriate term as it reflects a permanent microspecies, where the different races are capable of exchanging genes with one another, which has been adequately demonstrated in the different fruit forms observed in oil palm (Latiff, 2000). In fact, the characteristics of the three different races turn out to be controlled simply by the inheritance of a single gene. Genetic studies revealed that the shell gene shows co-dominant monogenic inheritance, which is exploitable in breeding programmes (Beirnaert and Vanderweyen, 1941).
The shell gene responsible for this phenotype was first reported in the Belgian Congo in the 1940's (Beirnaert and Venderweyan, 1941). However, tenera fruit forms were recognized and exploited in Africa well before then (Devuyst, 1953; Godding, 1930; Sousa et al., 2011). Given the central role played by the shell gene, oil palm breeding utilizes reciprocal recurrent selection of maternal (dura) and paternal (pisifera) pools using the North Carolina Model 1 maize breeding design (Rajanaidu el al., 2000). The Deli dura population, direct descendants of the four original African palms planted in Bogor Botanical Garden, Indonesia (1848), has excellent combining ability with the AVROS (Algemene Vereniging van Rubberplanters ter Oostkust van Sumatra) and other pisifera parental palms. AVROS pisifera palms were derived from the famous “Djongo” palm from Congo, but more recently several different accessions of dura and pisifera have also been sourced from Africa (Rajanaidu el al., 2000).
Tenera fruit types have a higher mesocarp to fruit ratio, which directly translates to significantly higher oil yield than either the dura or pisifera palm (as illustrated in Table 1).
TABLE 1Comparison of dura, tenera and pisifera fruit formsFruit FormCharacteristicDuraTeneraPisifera*Shell thickness (mm)2-80.5-3  Absence of shellFibre Ring**AbsentPresentAbsentMesocarp Content35-5560-9695(% fruit weight)Kernel Content 7-20 3-153-5(% fruit weight)Oil to Bunch (%)1626—Oil Yield (t/ha/yr)5.37.4—*usually female sterile, bunches rot prematurely**fibre ring is present in the mesocarp and often used as diagnostic tool to differentiate dura and tenera palms. (Source: Hardon et al., 1985; Hartley, 1988)
Since the crux of the breeding programmes in oil palm is to produce planting materials with higher oil yield, the tenera palm is the preferred choice for commercial planting. It is for this reason that substantial resources are invested by commercial seed producers to cross selected dura and pisifera palms in hybrid seed production. And despite the many advances which have been made in the production of hybrid oil palm seeds, two significant problems remain in the seed production process. First, batches of tenera seeds, which will produce the high oil yield tenera type palm, are often contaminated with dura seeds (Donough and Law, 1995). Today, it is estimated that dura contamination of tenera seeds can reach rates of approximately 5% (reduced from as high as 20-30% in the early 1990's as the result of improved quality control practices). Seed contamination is due in part to the difficulties of producing pure tenera seeds in open plantation conditions, where workers use ladders to manually pollinate tall trees, and where palm flowers for a given bunch mature over a period time, making it difficult to pollinate all flowers in a bunch with a single manual pollination event. Some flowers of the bunch may have matured prior to manual pollination and therefore may have had the opportunity to be wind pollinated from an unknown tree, thereby producing contaminant seeds in the bunch. Alternatively premature flowers may exist in the bunch at the time of manual pollination, and may mature after the pollination occurred allowing them to be wind pollinated from an unknown tree thereby producing contaminant seeds in the bunch. Prior to the invention described herein, it was not possible to identify the fruit type of a given seed of a given plant arising from a seed until it matured enough to produce a first batch of fruit, which typically takes approximately six years after germination. Notably, in the four to five years interval from germination to fruit production, significant land, labor, financial and energy resources are invested into what are believed to be tenera trees, some of which will ultimately be of the unwanted low yielding contaminant fruit types. By the time these suboptimal trees are identified, it is impractical to remove them from the field and replace them with tenera trees, and thus growers achieve lower palm oil yields for the 25 to 30 year production life of the contaminant trees. Therefore, the issue of contamination of batches of tenera seeds with dura or pisifera seeds is a problem for oil palm breeding, underscoring the need for a method to predict the fruit type of seeds and nursery plantlets with high accuracy.
A second problem in the seed production process is the investment seed producers make in maintaining dura and pisifera lines, and in the other expenses incurred in the hybrid seed production process. Prior to the present invention, there was no know way to produce a tree with an optimal shell phenotype which when crossed to itself or to another tree with optimal shell phenotype would produce seeds which would only generate optimal shell phenotypes. Therefore, there is a need to engineer trees to breed true from one generation to the next for optimal shell phenotype.
The genetic mapping of the shell gene was initially attempted by Mayes et al. (1997). A second group in Brazil, using a combination of bulked segregation analysis (BSA) and genetic mapping, reported two random amplified polymorphic DNA (RAPD) markers flanking the shell locus (Moretzsohn et al., 2000). More recently, Billotte et al., (2005) reported a simple sequence repeat (SSR)-based high density linkage map for oil palm, involving a cross between a thin shelled E. guineensis (tenera) palm and a thick shelled E. guineensis (dura) palm. A patent filed by the Malaysian Palm Oil Board (MPOB) describes the identification of a marker using restriction fragment technology, in particular a Restriction Fragment Length Polymorphism (RFLP) marker linked to the shell gene for plant identification and breeding purposes (RAJINDER SINGH, LESLIE OOI CHENG-LI, RAHIMAH A. RAHMAN AND LESLIE LOW ENG TI. 2008. Method for identification of a molecular marker linked to the shell gene of oil palm. Patent Application No. PI 20084563. Patent Filed on 13 Nov. 2008). The RFLP marker (SFB 83) was identified by way of generation or construction of a genetic map for a tenera fruit type palm.